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import unittest,os
import env
import pyopenms
from collections import defaultdict
eps = 2
def simple_find_best_feature(output, pairs, targeted):
f_map = defaultdict(list)
for f in output:
key = f.getMetaValue("PeptideRef")
f_map[key].append(f)
get_score = lambda f: f.getMetaValue("main_var_xx_lda_prelim_score")
for fl in f_map.values():
scores = [(get_score(fi), fi) for fi in fl]
best_score, best_feature = max(scores)
__, feature = scores[-1]
pep = targeted.getPeptideByRef(
feature.getMetaValue("PeptideRef")
)
pairs.append([best_feature.getRT(), pep.getRetentionTime()])
class TestMRMRTNormalizer(unittest.TestCase):
"""Emulates the behavior of OpenSwathMRMRTNormalizer"""
def setUp(self):
self.testdirname = os.path.join(env.OPEN_MS_SRC, "source/TEST/TOPP")
# set up files
self.chromatograms = os.path.join(self.testdirname, "OpenSwathRTNormalizer_1_input.mzML")
self.tramlfile = os.path.join(self.testdirname, "OpenSwathRTNormalizer_1_input.TraML")
def test_run_mrmrtnormalizer(self):
# load chromatograms
chromatograms = pyopenms.MSExperiment()
fh = pyopenms.FileHandler()
fh.loadExperiment(self.chromatograms, chromatograms)
# load TraML file
targeted = pyopenms.TargetedExperiment();
tramlfile = pyopenms.TraMLFile();
tramlfile.load(self.tramlfile, targeted);
# Create empty files as input and finally as output
empty_swath = pyopenms.MSExperiment()
trafo = pyopenms.TransformationDescription()
output = pyopenms.FeatureMap();
# set up featurefinder and run
featurefinder = pyopenms.MRMFeatureFinderScoring()
# set the correct rt use values
scoring_params = pyopenms.MRMFeatureFinderScoring().getDefaults();
scoring_params.setValue("Scores:use_rt_score", 'false', '')
featurefinder.setParameters(scoring_params);
featurefinder.pickExperiment(chromatograms, output, targeted, trafo, empty_swath)
# get the pairs
pairs=[]
simple_find_best_feature(output, pairs, targeted)
pairs_corrected = pyopenms.MRMRTNormalizer().rm_outliers( pairs, 0.95, 0.6)
pairs_corrected = [ list(p) for p in pairs_corrected]
expected = [(1497.56884765625, 1881.0),
(2045.9776611328125, 2409.0),
(2151.4814453125, 2509.0),
(1924.0750732421875, 2291.0),
(612.9832153320312, 990.0),
(1086.2474365234375, 1470.0),
(1133.89404296875, 1519.0),
(799.5291137695312, 1188.0),
(1397.1541748046875, 1765.0)]
for exp,res in zip(expected, pairs_corrected):
self.assertAlmostEqual(exp[0], res[0], eps)
self.assertAlmostEqual(exp[1], res[1], eps)
if __name__ == '__main__':
unittest.main()
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